Starting phenix.real_space_refine on Wed May 14 08:50:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zru_60405/05_2025/8zru_60405_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zru_60405/05_2025/8zru_60405.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zru_60405/05_2025/8zru_60405.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zru_60405/05_2025/8zru_60405.map" model { file = "/net/cci-nas-00/data/ceres_data/8zru_60405/05_2025/8zru_60405_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zru_60405/05_2025/8zru_60405_neut.cif" } resolution = 2.18 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 2 5.21 5 S 84 5.16 5 C 7452 2.51 5 N 1998 2.21 5 O 2280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 49 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 11816 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "B" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "C" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "D" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "E" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "F" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1969 Classifications: {'peptide': 260} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.92, per 1000 atoms: 0.59 Number of scatterers: 11816 At special positions: 0 Unit cell: (91.464, 98.88, 93.112, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 84 16.00 Mg 2 11.99 O 2280 8.00 N 1998 7.00 C 7452 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.5 seconds 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2868 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 12 sheets defined 57.4% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 62 through 78 Processing helix chain 'A' and resid 100 through 104 removed outlier: 3.568A pdb=" N GLN A 104 " --> pdb=" O LYS A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 113 Processing helix chain 'A' and resid 118 through 126 removed outlier: 4.092A pdb=" N ASP A 121 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N HIS A 122 " --> pdb=" O HIS A 119 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU A 123 " --> pdb=" O TRP A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 148 Processing helix chain 'A' and resid 162 through 168 removed outlier: 4.308A pdb=" N ILE A 165 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 168 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 184 Processing helix chain 'A' and resid 184 through 195 removed outlier: 3.553A pdb=" N ALA A 188 " --> pdb=" O GLY A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 207 Processing helix chain 'A' and resid 217 through 231 Processing helix chain 'A' and resid 233 through 246 Processing helix chain 'A' and resid 247 through 249 No H-bonds generated for 'chain 'A' and resid 247 through 249' Processing helix chain 'A' and resid 251 through 266 Processing helix chain 'A' and resid 269 through 281 removed outlier: 4.036A pdb=" N LYS A 273 " --> pdb=" O THR A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 62 through 78 Processing helix chain 'B' and resid 100 through 105 removed outlier: 4.787A pdb=" N ASN B 105 " --> pdb=" O LYS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 removed outlier: 3.725A pdb=" N SER B 114 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 126 removed outlier: 4.169A pdb=" N ASP B 121 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N HIS B 122 " --> pdb=" O HIS B 119 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU B 123 " --> pdb=" O TRP B 120 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL B 126 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 149 removed outlier: 3.608A pdb=" N CYS B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 162 through 168 removed outlier: 4.297A pdb=" N ILE B 165 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY B 168 " --> pdb=" O ILE B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 184 Processing helix chain 'B' and resid 184 through 195 removed outlier: 3.533A pdb=" N ALA B 188 " --> pdb=" O GLY B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 206 Processing helix chain 'B' and resid 217 through 231 Processing helix chain 'B' and resid 233 through 246 Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 251 through 267 removed outlier: 3.875A pdb=" N PHE B 267 " --> pdb=" O PHE B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 281 removed outlier: 3.788A pdb=" N LYS B 273 " --> pdb=" O THR B 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 45 Processing helix chain 'C' and resid 62 through 78 Processing helix chain 'C' and resid 107 through 113 Processing helix chain 'C' and resid 117 through 126 removed outlier: 3.736A pdb=" N ASP C 121 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS C 122 " --> pdb=" O HIS C 119 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LEU C 123 " --> pdb=" O TRP C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 149 removed outlier: 3.602A pdb=" N CYS C 149 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 162 through 168 removed outlier: 4.297A pdb=" N ILE C 165 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY C 168 " --> pdb=" O ILE C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 184 Processing helix chain 'C' and resid 184 through 195 Processing helix chain 'C' and resid 200 through 206 Processing helix chain 'C' and resid 214 through 216 No H-bonds generated for 'chain 'C' and resid 214 through 216' Processing helix chain 'C' and resid 217 through 231 Processing helix chain 'C' and resid 233 through 246 Processing helix chain 'C' and resid 247 through 249 No H-bonds generated for 'chain 'C' and resid 247 through 249' Processing helix chain 'C' and resid 251 through 266 Processing helix chain 'C' and resid 269 through 281 removed outlier: 3.884A pdb=" N LYS C 273 " --> pdb=" O THR C 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 62 through 78 Processing helix chain 'D' and resid 99 through 105 removed outlier: 3.781A pdb=" N MET D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ASN D 105 " --> pdb=" O LYS D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 113 Processing helix chain 'D' and resid 117 through 126 removed outlier: 3.997A pdb=" N ASP D 121 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS D 122 " --> pdb=" O HIS D 119 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N LEU D 123 " --> pdb=" O TRP D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 148 Processing helix chain 'D' and resid 162 through 168 removed outlier: 4.260A pdb=" N ILE D 165 " --> pdb=" O GLN D 162 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY D 168 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 184 Processing helix chain 'D' and resid 184 through 195 removed outlier: 3.568A pdb=" N ALA D 188 " --> pdb=" O GLY D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 207 Processing helix chain 'D' and resid 217 through 231 Processing helix chain 'D' and resid 233 through 246 Processing helix chain 'D' and resid 247 through 249 No H-bonds generated for 'chain 'D' and resid 247 through 249' Processing helix chain 'D' and resid 251 through 266 Processing helix chain 'D' and resid 269 through 281 removed outlier: 3.886A pdb=" N LYS D 273 " --> pdb=" O THR D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 45 Processing helix chain 'E' and resid 62 through 78 Processing helix chain 'E' and resid 100 through 104 removed outlier: 3.822A pdb=" N GLN E 104 " --> pdb=" O LYS E 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 113 Processing helix chain 'E' and resid 118 through 126 removed outlier: 3.765A pdb=" N ASP E 121 " --> pdb=" O LYS E 118 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N HIS E 122 " --> pdb=" O HIS E 119 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU E 123 " --> pdb=" O TRP E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 149 removed outlier: 3.575A pdb=" N CYS E 149 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 168 removed outlier: 4.297A pdb=" N ILE E 165 " --> pdb=" O GLN E 162 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLY E 168 " --> pdb=" O ILE E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 184 Processing helix chain 'E' and resid 184 through 195 removed outlier: 3.551A pdb=" N ALA E 188 " --> pdb=" O GLY E 184 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 206 Processing helix chain 'E' and resid 217 through 231 Processing helix chain 'E' and resid 233 through 246 Processing helix chain 'E' and resid 247 through 249 No H-bonds generated for 'chain 'E' and resid 247 through 249' Processing helix chain 'E' and resid 251 through 266 Processing helix chain 'E' and resid 269 through 281 removed outlier: 3.948A pdb=" N LYS E 273 " --> pdb=" O THR E 269 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 45 Processing helix chain 'F' and resid 62 through 78 Processing helix chain 'F' and resid 100 through 105 removed outlier: 4.739A pdb=" N ASN F 105 " --> pdb=" O LYS F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 113 Processing helix chain 'F' and resid 118 through 126 removed outlier: 4.017A pdb=" N ASP F 121 " --> pdb=" O LYS F 118 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N HIS F 122 " --> pdb=" O HIS F 119 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N LEU F 123 " --> pdb=" O TRP F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 149 removed outlier: 3.578A pdb=" N CYS F 149 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 168 removed outlier: 4.273A pdb=" N ILE F 165 " --> pdb=" O GLN F 162 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY F 168 " --> pdb=" O ILE F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 184 Processing helix chain 'F' and resid 184 through 195 removed outlier: 3.530A pdb=" N ALA F 188 " --> pdb=" O GLY F 184 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 206 Processing helix chain 'F' and resid 217 through 231 Processing helix chain 'F' and resid 233 through 246 Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 251 through 267 removed outlier: 3.850A pdb=" N PHE F 267 " --> pdb=" O PHE F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 281 removed outlier: 3.883A pdb=" N LYS F 273 " --> pdb=" O THR F 269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 41 removed outlier: 3.540A pdb=" N VAL A 47 " --> pdb=" O ARG A 41 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY A 48 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N THR A 88 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE A 50 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE A 85 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N ALA A 133 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU A 87 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL A 130 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N TYR A 153 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ALA A 132 " --> pdb=" O TYR A 153 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLY A 155 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N VAL A 134 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ILE A 152 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N CYS A 213 " --> pdb=" O ILE A 152 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ALA A 154 " --> pdb=" O CYS A 213 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 95 removed outlier: 7.565A pdb=" N PHE A 139 " --> pdb=" O PHE A 94 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 41 removed outlier: 6.294A pdb=" N GLY B 48 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N THR B 88 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ILE B 50 " --> pdb=" O THR B 88 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE B 85 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N ALA B 133 " --> pdb=" O ILE B 85 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU B 87 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL B 130 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N TYR B 153 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ALA B 132 " --> pdb=" O TYR B 153 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLY B 155 " --> pdb=" O ALA B 132 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N VAL B 134 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE B 152 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N CYS B 213 " --> pdb=" O ILE B 152 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA B 154 " --> pdb=" O CYS B 213 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 93 through 95 removed outlier: 7.538A pdb=" N PHE B 139 " --> pdb=" O PHE B 94 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 36 through 41 removed outlier: 3.612A pdb=" N VAL C 47 " --> pdb=" O ARG C 41 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N GLY C 48 " --> pdb=" O VAL C 86 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR C 88 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE C 50 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE C 85 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ALA C 133 " --> pdb=" O ILE C 85 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU C 87 " --> pdb=" O ALA C 133 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL C 130 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N TYR C 153 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N ALA C 132 " --> pdb=" O TYR C 153 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS C 211 " --> pdb=" O ILE C 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 93 through 95 removed outlier: 7.561A pdb=" N PHE C 139 " --> pdb=" O PHE C 94 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 36 through 41 removed outlier: 3.596A pdb=" N VAL D 47 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLY D 48 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N THR D 88 " --> pdb=" O GLY D 48 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE D 50 " --> pdb=" O THR D 88 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE D 85 " --> pdb=" O ILE D 131 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N ALA D 133 " --> pdb=" O ILE D 85 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU D 87 " --> pdb=" O ALA D 133 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL D 130 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N TYR D 153 " --> pdb=" O VAL D 130 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N ALA D 132 " --> pdb=" O TYR D 153 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS D 211 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 93 through 95 removed outlier: 7.580A pdb=" N PHE D 139 " --> pdb=" O PHE D 94 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 36 through 41 removed outlier: 3.616A pdb=" N VAL E 47 " --> pdb=" O ARG E 41 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N GLY E 48 " --> pdb=" O VAL E 86 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR E 88 " --> pdb=" O GLY E 48 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE E 50 " --> pdb=" O THR E 88 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N ILE E 85 " --> pdb=" O ILE E 131 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N ALA E 133 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LEU E 87 " --> pdb=" O ALA E 133 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL E 130 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N TYR E 153 " --> pdb=" O VAL E 130 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ALA E 132 " --> pdb=" O TYR E 153 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLY E 155 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N VAL E 134 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N ILE E 152 " --> pdb=" O LYS E 211 " (cutoff:3.500A) removed outlier: 8.335A pdb=" N CYS E 213 " --> pdb=" O ILE E 152 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA E 154 " --> pdb=" O CYS E 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 93 through 95 removed outlier: 7.584A pdb=" N PHE E 139 " --> pdb=" O PHE E 94 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 36 through 41 removed outlier: 3.651A pdb=" N VAL F 47 " --> pdb=" O ARG F 41 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N GLY F 48 " --> pdb=" O VAL F 86 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N THR F 88 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE F 50 " --> pdb=" O THR F 88 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N ILE F 85 " --> pdb=" O ILE F 131 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N ALA F 133 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU F 87 " --> pdb=" O ALA F 133 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL F 130 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N TYR F 153 " --> pdb=" O VAL F 130 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N ALA F 132 " --> pdb=" O TYR F 153 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N GLY F 155 " --> pdb=" O ALA F 132 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N VAL F 134 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE F 152 " --> pdb=" O LYS F 211 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N CYS F 213 " --> pdb=" O ILE F 152 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N ALA F 154 " --> pdb=" O CYS F 213 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 93 through 95 removed outlier: 5.317A pdb=" N TYR F 137 " --> pdb=" O ALA F 93 " (cutoff:3.500A) 572 hydrogen bonds defined for protein. 1578 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.33 Time building geometry restraints manager: 2.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 2103 1.30 - 1.43: 2641 1.43 - 1.56: 7092 1.56 - 1.68: 2 1.68 - 1.81: 132 Bond restraints: 11970 Sorted by residual: bond pdb=" CA SER E 113 " pdb=" C SER E 113 " ideal model delta sigma weight residual 1.526 1.447 0.080 1.11e-02 8.12e+03 5.15e+01 bond pdb=" CA SER B 113 " pdb=" C SER B 113 " ideal model delta sigma weight residual 1.524 1.447 0.077 1.24e-02 6.50e+03 3.87e+01 bond pdb=" N SER E 113 " pdb=" CA SER E 113 " ideal model delta sigma weight residual 1.462 1.383 0.079 1.38e-02 5.25e+03 3.26e+01 bond pdb=" N SER D 113 " pdb=" CA SER D 113 " ideal model delta sigma weight residual 1.455 1.382 0.074 1.30e-02 5.92e+03 3.20e+01 bond pdb=" C SER D 113 " pdb=" O SER D 113 " ideal model delta sigma weight residual 1.234 1.174 0.061 1.23e-02 6.61e+03 2.45e+01 ... (remaining 11965 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 15997 2.84 - 5.69: 78 5.69 - 8.53: 19 8.53 - 11.37: 1 11.37 - 14.22: 3 Bond angle restraints: 16098 Sorted by residual: angle pdb=" N SER D 113 " pdb=" CA SER D 113 " pdb=" C SER D 113 " ideal model delta sigma weight residual 110.20 95.98 14.22 1.58e+00 4.01e-01 8.10e+01 angle pdb=" N PHE C 116 " pdb=" CA PHE C 116 " pdb=" C PHE C 116 " ideal model delta sigma weight residual 111.37 125.30 -13.93 1.64e+00 3.72e-01 7.22e+01 angle pdb=" N SER B 113 " pdb=" CA SER B 113 " pdb=" C SER B 113 " ideal model delta sigma weight residual 111.03 119.44 -8.41 1.11e+00 8.12e-01 5.74e+01 angle pdb=" N SER E 114 " pdb=" CA SER E 114 " pdb=" C SER E 114 " ideal model delta sigma weight residual 110.80 98.76 12.04 2.13e+00 2.20e-01 3.20e+01 angle pdb=" C SER E 113 " pdb=" CA SER E 113 " pdb=" CB SER E 113 " ideal model delta sigma weight residual 112.05 103.67 8.38 1.52e+00 4.33e-01 3.04e+01 ... (remaining 16093 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 6665 17.97 - 35.94: 444 35.94 - 53.91: 159 53.91 - 71.88: 50 71.88 - 89.85: 14 Dihedral angle restraints: 7332 sinusoidal: 2880 harmonic: 4452 Sorted by residual: dihedral pdb=" C LYS D 115 " pdb=" N LYS D 115 " pdb=" CA LYS D 115 " pdb=" CB LYS D 115 " ideal model delta harmonic sigma weight residual -122.60 -136.51 13.91 0 2.50e+00 1.60e-01 3.10e+01 dihedral pdb=" N SER D 114 " pdb=" C SER D 114 " pdb=" CA SER D 114 " pdb=" CB SER D 114 " ideal model delta harmonic sigma weight residual 122.80 136.34 -13.54 0 2.50e+00 1.60e-01 2.93e+01 dihedral pdb=" N SER C 114 " pdb=" C SER C 114 " pdb=" CA SER C 114 " pdb=" CB SER C 114 " ideal model delta harmonic sigma weight residual 122.80 135.30 -12.50 0 2.50e+00 1.60e-01 2.50e+01 ... (remaining 7329 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.133: 1809 0.133 - 0.267: 13 0.267 - 0.400: 9 0.400 - 0.534: 3 0.534 - 0.667: 2 Chirality restraints: 1836 Sorted by residual: chirality pdb=" CA LYS D 115 " pdb=" N LYS D 115 " pdb=" C LYS D 115 " pdb=" CB LYS D 115 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA LYS C 115 " pdb=" N LYS C 115 " pdb=" C LYS C 115 " pdb=" CB LYS C 115 " both_signs ideal model delta sigma weight residual False 2.51 1.96 0.55 2.00e-01 2.50e+01 7.58e+00 chirality pdb=" CA PHE C 116 " pdb=" N PHE C 116 " pdb=" C PHE C 116 " pdb=" CB PHE C 116 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.76e+00 ... (remaining 1833 not shown) Planarity restraints: 2094 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS E 111 " 0.014 2.00e-02 2.50e+03 2.73e-02 7.44e+00 pdb=" C CYS E 111 " -0.047 2.00e-02 2.50e+03 pdb=" O CYS E 111 " 0.017 2.00e-02 2.50e+03 pdb=" N TYR E 112 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 118 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.40e+00 pdb=" C LYS C 118 " 0.032 2.00e-02 2.50e+03 pdb=" O LYS C 118 " -0.012 2.00e-02 2.50e+03 pdb=" N HIS C 119 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 118 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C LYS E 118 " -0.030 2.00e-02 2.50e+03 pdb=" O LYS E 118 " 0.011 2.00e-02 2.50e+03 pdb=" N HIS E 119 " 0.010 2.00e-02 2.50e+03 ... (remaining 2091 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2010 2.76 - 3.30: 11215 3.30 - 3.83: 20858 3.83 - 4.37: 25091 4.37 - 4.90: 42142 Nonbonded interactions: 101316 Sorted by model distance: nonbonded pdb=" N ASP B 270 " pdb=" OD1 ASP B 270 " model vdw 2.230 3.120 nonbonded pdb=" O GLU F 190 " pdb=" OG1 THR F 194 " model vdw 2.287 3.040 nonbonded pdb=" O PHE B 263 " pdb=" OG1 THR B 266 " model vdw 2.293 3.040 nonbonded pdb=" O GLU B 190 " pdb=" OG1 THR B 194 " model vdw 2.298 3.040 nonbonded pdb=" O GLU A 190 " pdb=" OG1 THR A 194 " model vdw 2.298 3.040 ... (remaining 101311 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = (chain 'C' and resid 31 through 290) selection = (chain 'D' and resid 31 through 290) selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.800 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 11970 Z= 0.261 Angle : 0.587 14.217 16098 Z= 0.372 Chirality : 0.054 0.667 1836 Planarity : 0.002 0.027 2094 Dihedral : 15.385 89.846 4464 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.20 % Favored : 97.74 % Rotamer: Outliers : 1.06 % Allowed : 12.68 % Favored : 86.26 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.18), residues: 1548 helix: -0.04 (0.18), residues: 690 sheet: -0.20 (0.46), residues: 144 loop : -1.74 (0.18), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP C 120 HIS 0.002 0.000 HIS C 119 PHE 0.010 0.001 PHE C 116 TYR 0.015 0.001 TYR B 112 ARG 0.001 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.15325 ( 572) hydrogen bonds : angle 6.71794 ( 1578) covalent geometry : bond 0.00374 (11970) covalent geometry : angle 0.58660 (16098) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 278 time to evaluate : 1.391 Fit side-chains REVERT: A 191 MET cc_start: 0.7249 (mtp) cc_final: 0.7045 (mtp) REVERT: A 220 GLU cc_start: 0.4925 (mm-30) cc_final: 0.4702 (mm-30) REVERT: A 221 GLU cc_start: 0.6492 (mp0) cc_final: 0.5978 (mt-10) REVERT: A 224 GLN cc_start: 0.6026 (mt0) cc_final: 0.5684 (mt0) REVERT: A 242 GLU cc_start: 0.6906 (mt-10) cc_final: 0.6609 (mt-10) REVERT: A 249 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7106 (mm-30) REVERT: A 282 LYS cc_start: 0.7298 (OUTLIER) cc_final: 0.6962 (mmtm) REVERT: B 92 LYS cc_start: 0.6159 (mmtm) cc_final: 0.5736 (mmmt) REVERT: B 205 GLN cc_start: 0.5854 (pp30) cc_final: 0.5122 (pt0) REVERT: B 239 MET cc_start: 0.7177 (mtt) cc_final: 0.6657 (mtp) REVERT: C 144 GLU cc_start: 0.6538 (mt-10) cc_final: 0.6192 (mt-10) REVERT: D 77 GLU cc_start: 0.6324 (tp30) cc_final: 0.6018 (mm-30) REVERT: D 103 MET cc_start: 0.7506 (ptm) cc_final: 0.7060 (ptm) REVERT: D 108 PHE cc_start: 0.7103 (t80) cc_final: 0.6826 (t80) REVERT: D 121 ASP cc_start: 0.6977 (m-30) cc_final: 0.5996 (p0) REVERT: D 156 GLU cc_start: 0.7137 (mm-30) cc_final: 0.6453 (tp30) REVERT: D 211 LYS cc_start: 0.7848 (tttp) cc_final: 0.7163 (tttt) REVERT: D 239 MET cc_start: 0.7111 (mtt) cc_final: 0.6862 (mtp) REVERT: E 99 ASP cc_start: 0.6348 (t0) cc_final: 0.5712 (t70) REVERT: E 115 LYS cc_start: 0.5937 (OUTLIER) cc_final: 0.5542 (mttt) REVERT: E 224 GLN cc_start: 0.6091 (mt0) cc_final: 0.5792 (mt0) REVERT: E 282 LYS cc_start: 0.7313 (OUTLIER) cc_final: 0.6888 (ptpp) REVERT: F 41 ARG cc_start: 0.6491 (mmm-85) cc_final: 0.6236 (mmt90) REVERT: F 121 ASP cc_start: 0.7124 (m-30) cc_final: 0.6019 (p0) REVERT: F 147 MET cc_start: 0.7384 (mtm) cc_final: 0.7118 (mtm) REVERT: F 156 GLU cc_start: 0.6496 (pt0) cc_final: 0.6207 (mt-10) REVERT: F 205 GLN cc_start: 0.5798 (pp30) cc_final: 0.5045 (pt0) REVERT: F 239 MET cc_start: 0.7209 (mtt) cc_final: 0.6823 (mtp) outliers start: 13 outliers final: 5 residues processed: 288 average time/residue: 1.4227 time to fit residues: 438.3255 Evaluate side-chains 218 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 210 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 LYS Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 114 SER Chi-restraints excluded: chain C residue 118 LYS Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 282 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 131 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 40 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 63 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 141 optimal weight: 0.6980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 104 GLN A 162 GLN A 205 GLN A 224 GLN B 104 GLN B 119 HIS B 162 GLN C 104 GLN C 105 ASN C 125 GLN C 162 GLN C 205 GLN C 224 GLN C 286 ASN D 104 GLN D 125 GLN D 162 GLN E 104 GLN E 162 GLN E 224 GLN F 104 GLN F 162 GLN F 224 GLN F 286 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.148998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.126313 restraints weight = 10426.970| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 1.10 r_work: 0.3352 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8632 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 11970 Z= 0.164 Angle : 0.557 5.111 16098 Z= 0.307 Chirality : 0.045 0.140 1836 Planarity : 0.004 0.040 2094 Dihedral : 5.746 59.264 1655 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.52 % Favored : 97.42 % Rotamer: Outliers : 2.44 % Allowed : 13.82 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.20), residues: 1548 helix: 1.06 (0.19), residues: 738 sheet: 0.47 (0.47), residues: 150 loop : -0.94 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 120 HIS 0.002 0.001 HIS E 119 PHE 0.014 0.002 PHE F 139 TYR 0.012 0.002 TYR C 112 ARG 0.006 0.001 ARG A 54 Details of bonding type rmsd hydrogen bonds : bond 0.04737 ( 572) hydrogen bonds : angle 4.75687 ( 1578) covalent geometry : bond 0.00357 (11970) covalent geometry : angle 0.55737 (16098) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 1.224 Fit side-chains REVERT: A 77 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7363 (mm-30) REVERT: A 103 MET cc_start: 0.8309 (ptp) cc_final: 0.8055 (ptt) REVERT: A 108 PHE cc_start: 0.8166 (t80) cc_final: 0.7905 (t80) REVERT: A 216 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7338 (mp0) REVERT: A 250 MET cc_start: 0.9182 (ptp) cc_final: 0.8942 (ptp) REVERT: B 92 LYS cc_start: 0.8015 (mmtm) cc_final: 0.7609 (mmmt) REVERT: B 239 MET cc_start: 0.9099 (mtt) cc_final: 0.8881 (mtp) REVERT: D 156 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7834 (tp30) REVERT: D 205 GLN cc_start: 0.8046 (tp-100) cc_final: 0.7838 (tm130) REVERT: E 77 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7388 (mm-30) REVERT: E 108 PHE cc_start: 0.8146 (t80) cc_final: 0.7828 (t80) REVERT: E 115 LYS cc_start: 0.7321 (OUTLIER) cc_final: 0.6553 (mttt) REVERT: E 220 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7756 (mp0) REVERT: E 282 LYS cc_start: 0.7622 (mptt) cc_final: 0.7252 (ptpp) REVERT: F 77 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7615 (mm-30) REVERT: F 92 LYS cc_start: 0.8061 (mmpt) cc_final: 0.7779 (mmmt) REVERT: F 103 MET cc_start: 0.8164 (ptp) cc_final: 0.7950 (ptt) REVERT: F 205 GLN cc_start: 0.7951 (pp30) cc_final: 0.7736 (pt0) outliers start: 30 outliers final: 6 residues processed: 247 average time/residue: 1.4055 time to fit residues: 371.6686 Evaluate side-chains 224 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 213 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 231 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 76 optimal weight: 9.9990 chunk 94 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 131 optimal weight: 0.0770 chunk 115 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 75 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 92 optimal weight: 0.0370 overall best weight: 0.6020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 224 GLN B 125 GLN C 53 ASN C 205 GLN D 119 HIS D 125 GLN E 224 GLN F 53 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.152816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.130078 restraints weight = 10667.121| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 1.12 r_work: 0.3417 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11970 Z= 0.083 Angle : 0.422 5.138 16098 Z= 0.233 Chirality : 0.041 0.136 1836 Planarity : 0.002 0.025 2094 Dihedral : 4.227 41.679 1636 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 1.49 % Favored : 98.45 % Rotamer: Outliers : 1.22 % Allowed : 16.02 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.21), residues: 1548 helix: 1.44 (0.20), residues: 738 sheet: 0.69 (0.48), residues: 150 loop : -0.69 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 120 HIS 0.003 0.001 HIS D 119 PHE 0.009 0.001 PHE B 108 TYR 0.011 0.001 TYR F 112 ARG 0.002 0.000 ARG F 272 Details of bonding type rmsd hydrogen bonds : bond 0.03191 ( 572) hydrogen bonds : angle 4.33793 ( 1578) covalent geometry : bond 0.00167 (11970) covalent geometry : angle 0.42246 (16098) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 1.394 Fit side-chains REVERT: A 108 PHE cc_start: 0.8180 (t80) cc_final: 0.7893 (t80) REVERT: B 121 ASP cc_start: 0.7853 (m-30) cc_final: 0.7324 (p0) REVERT: B 216 GLU cc_start: 0.8006 (pm20) cc_final: 0.7802 (pm20) REVERT: C 77 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7479 (mm-30) REVERT: D 121 ASP cc_start: 0.7879 (m-30) cc_final: 0.7406 (p0) REVERT: D 156 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7753 (tp30) REVERT: E 108 PHE cc_start: 0.8147 (t80) cc_final: 0.7911 (t80) REVERT: E 220 GLU cc_start: 0.8329 (mm-30) cc_final: 0.7752 (mp0) REVERT: F 77 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7580 (mm-30) REVERT: F 92 LYS cc_start: 0.7949 (mmpt) cc_final: 0.7735 (mmmt) REVERT: F 101 LYS cc_start: 0.7691 (mmmm) cc_final: 0.7218 (mptt) REVERT: F 121 ASP cc_start: 0.7793 (m-30) cc_final: 0.7254 (p0) outliers start: 15 outliers final: 4 residues processed: 219 average time/residue: 1.4582 time to fit residues: 341.7748 Evaluate side-chains 209 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 203 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 237 VAL Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain F residue 77 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 103 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 111 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 35 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 125 GLN C 205 GLN D 125 GLN F 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.146958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.124215 restraints weight = 10512.578| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.11 r_work: 0.3326 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11970 Z= 0.180 Angle : 0.550 4.522 16098 Z= 0.307 Chirality : 0.046 0.145 1836 Planarity : 0.004 0.033 2094 Dihedral : 4.934 24.705 1632 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.39 % Favored : 97.55 % Rotamer: Outliers : 2.11 % Allowed : 13.82 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1548 helix: 1.35 (0.20), residues: 738 sheet: 0.76 (0.48), residues: 150 loop : -0.63 (0.20), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP E 120 HIS 0.002 0.001 HIS B 119 PHE 0.012 0.002 PHE D 33 TYR 0.013 0.002 TYR F 112 ARG 0.004 0.001 ARG F 197 Details of bonding type rmsd hydrogen bonds : bond 0.04782 ( 572) hydrogen bonds : angle 4.65615 ( 1578) covalent geometry : bond 0.00400 (11970) covalent geometry : angle 0.54975 (16098) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 1.229 Fit side-chains REVERT: A 77 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7452 (mm-30) REVERT: A 108 PHE cc_start: 0.8211 (t80) cc_final: 0.7951 (t80) REVERT: A 216 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: A 220 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7523 (mp0) REVERT: B 77 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.7513 (mm-30) REVERT: B 216 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7814 (pm20) REVERT: C 77 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7544 (mm-30) REVERT: D 77 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7516 (mm-30) REVERT: D 211 LYS cc_start: 0.9125 (OUTLIER) cc_final: 0.8913 (tttp) REVERT: E 77 GLU cc_start: 0.8153 (OUTLIER) cc_final: 0.7446 (mm-30) REVERT: E 108 PHE cc_start: 0.8190 (t80) cc_final: 0.7932 (t80) REVERT: E 156 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: E 216 GLU cc_start: 0.7917 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: E 220 GLU cc_start: 0.8340 (mm-30) cc_final: 0.7810 (mp0) REVERT: F 77 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7587 (mm-30) outliers start: 26 outliers final: 7 residues processed: 228 average time/residue: 1.4318 time to fit residues: 349.5269 Evaluate side-chains 211 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 193 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 211 LYS Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 231 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 15 optimal weight: 10.0000 chunk 148 optimal weight: 0.0770 chunk 84 optimal weight: 9.9990 chunk 150 optimal weight: 9.9990 chunk 29 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 65 optimal weight: 0.9980 chunk 67 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN B 125 GLN C 53 ASN C 205 GLN D 125 GLN D 205 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.147888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.125146 restraints weight = 10434.599| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 1.11 r_work: 0.3339 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11970 Z= 0.134 Angle : 0.493 5.304 16098 Z= 0.275 Chirality : 0.044 0.131 1836 Planarity : 0.003 0.034 2094 Dihedral : 4.848 27.721 1632 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.44 % Allowed : 12.93 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.21), residues: 1548 helix: 1.40 (0.20), residues: 738 sheet: 0.81 (0.48), residues: 150 loop : -0.56 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP F 120 HIS 0.003 0.001 HIS D 119 PHE 0.009 0.001 PHE B 94 TYR 0.013 0.001 TYR F 112 ARG 0.003 0.001 ARG F 272 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 572) hydrogen bonds : angle 4.49252 ( 1578) covalent geometry : bond 0.00292 (11970) covalent geometry : angle 0.49320 (16098) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 1.362 Fit side-chains REVERT: A 77 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7453 (mm-30) REVERT: A 101 LYS cc_start: 0.7818 (mmtt) cc_final: 0.7393 (ptpp) REVERT: A 108 PHE cc_start: 0.8204 (t80) cc_final: 0.7928 (t80) REVERT: A 216 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: A 220 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7510 (mp0) REVERT: B 77 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7496 (mm-30) REVERT: B 121 ASP cc_start: 0.7901 (m-30) cc_final: 0.7353 (p0) REVERT: B 216 GLU cc_start: 0.8034 (pm20) cc_final: 0.7815 (pm20) REVERT: C 77 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7502 (mm-30) REVERT: D 77 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7535 (mm-30) REVERT: D 115 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6408 (mttt) REVERT: D 121 ASP cc_start: 0.7905 (m-30) cc_final: 0.7313 (p0) REVERT: E 77 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7416 (mm-30) REVERT: E 118 LYS cc_start: 0.7720 (pmtt) cc_final: 0.7308 (ptmt) REVERT: E 156 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: E 215 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8434 (t) REVERT: E 216 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: E 220 GLU cc_start: 0.8312 (mm-30) cc_final: 0.7801 (mp0) REVERT: F 77 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: F 101 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7337 (mptt) REVERT: F 121 ASP cc_start: 0.7844 (m-30) cc_final: 0.7273 (p0) outliers start: 30 outliers final: 7 residues processed: 211 average time/residue: 1.5734 time to fit residues: 353.8258 Evaluate side-chains 206 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 156 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 231 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 138 optimal weight: 10.0000 chunk 52 optimal weight: 10.0000 chunk 100 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN B 286 ASN C 205 GLN D 44 ASN D 125 GLN D 205 GLN F 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.145914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.123232 restraints weight = 10509.261| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.12 r_work: 0.3314 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3209 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11970 Z= 0.196 Angle : 0.564 5.075 16098 Z= 0.316 Chirality : 0.047 0.146 1836 Planarity : 0.004 0.038 2094 Dihedral : 5.289 29.652 1632 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.03 % Allowed : 13.17 % Favored : 84.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.21), residues: 1548 helix: 1.29 (0.19), residues: 738 sheet: 0.78 (0.48), residues: 150 loop : -0.57 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP F 120 HIS 0.002 0.001 HIS C 119 PHE 0.011 0.002 PHE D 33 TYR 0.013 0.002 TYR E 112 ARG 0.004 0.001 ARG F 197 Details of bonding type rmsd hydrogen bonds : bond 0.04976 ( 572) hydrogen bonds : angle 4.68852 ( 1578) covalent geometry : bond 0.00437 (11970) covalent geometry : angle 0.56369 (16098) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 194 time to evaluate : 1.331 Fit side-chains REVERT: A 77 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7489 (mm-30) REVERT: A 101 LYS cc_start: 0.7842 (mmtt) cc_final: 0.7456 (ptpp) REVERT: A 108 PHE cc_start: 0.8213 (t80) cc_final: 0.7920 (t80) REVERT: A 216 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7322 (mp0) REVERT: A 220 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7699 (mp0) REVERT: B 77 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.7519 (mm-30) REVERT: B 216 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7817 (pm20) REVERT: C 77 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7543 (mm-30) REVERT: D 77 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7569 (mm-30) REVERT: D 115 LYS cc_start: 0.7250 (OUTLIER) cc_final: 0.6428 (mttt) REVERT: E 77 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7453 (mm-30) REVERT: E 108 PHE cc_start: 0.8209 (t80) cc_final: 0.7996 (t80) REVERT: E 215 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8527 (t) REVERT: E 216 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: E 220 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7816 (mp0) REVERT: F 77 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: F 92 LYS cc_start: 0.8052 (mmtm) cc_final: 0.7724 (mmmt) REVERT: F 101 LYS cc_start: 0.7766 (OUTLIER) cc_final: 0.7275 (mptt) REVERT: F 239 MET cc_start: 0.9129 (mtt) cc_final: 0.8898 (mtp) outliers start: 25 outliers final: 10 residues processed: 209 average time/residue: 1.5387 time to fit residues: 343.2241 Evaluate side-chains 215 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 115 LYS Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 231 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 20 optimal weight: 4.9990 chunk 126 optimal weight: 8.9990 chunk 7 optimal weight: 6.9990 chunk 73 optimal weight: 4.9990 chunk 154 optimal weight: 9.9990 chunk 61 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 149 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 21 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN C 205 GLN D 53 ASN D 125 GLN D 286 ASN F 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.143984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.121467 restraints weight = 10488.696| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.11 r_work: 0.3287 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 11970 Z= 0.314 Angle : 0.702 5.417 16098 Z= 0.395 Chirality : 0.054 0.203 1836 Planarity : 0.005 0.052 2094 Dihedral : 5.871 33.187 1632 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.20 % Allowed : 12.68 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.20), residues: 1548 helix: 0.96 (0.19), residues: 738 sheet: 0.74 (0.49), residues: 150 loop : -0.69 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP C 120 HIS 0.003 0.001 HIS E 122 PHE 0.016 0.003 PHE D 279 TYR 0.017 0.003 TYR B 35 ARG 0.007 0.001 ARG F 197 Details of bonding type rmsd hydrogen bonds : bond 0.06080 ( 572) hydrogen bonds : angle 5.00369 ( 1578) covalent geometry : bond 0.00710 (11970) covalent geometry : angle 0.70173 (16098) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 1.254 Fit side-chains REVERT: A 77 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7502 (mm-30) REVERT: A 101 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7565 (ptpp) REVERT: A 108 PHE cc_start: 0.8234 (t80) cc_final: 0.7956 (t80) REVERT: A 156 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7776 (mm-30) REVERT: A 216 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: A 220 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7875 (mp0) REVERT: B 77 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7581 (mm-30) REVERT: C 77 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: D 77 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7596 (mm-30) REVERT: D 156 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7587 (mm-30) REVERT: E 77 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7492 (mm-30) REVERT: E 220 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7816 (mp0) REVERT: E 282 LYS cc_start: 0.7787 (mptt) cc_final: 0.7350 (ptpp) REVERT: F 77 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7625 (mm-30) REVERT: F 101 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7242 (mptt) REVERT: F 282 LYS cc_start: 0.7780 (OUTLIER) cc_final: 0.7488 (ptpp) outliers start: 27 outliers final: 9 residues processed: 208 average time/residue: 1.4652 time to fit residues: 326.1729 Evaluate side-chains 207 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 156 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain D residue 156 GLU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 118 LYS Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 282 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 23 optimal weight: 2.9990 chunk 118 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 136 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 121 optimal weight: 3.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN D 125 GLN D 205 GLN F 53 ASN F 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.146723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124085 restraints weight = 10471.577| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.11 r_work: 0.3324 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 2.69 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11970 Z= 0.150 Angle : 0.523 5.707 16098 Z= 0.293 Chirality : 0.045 0.131 1836 Planarity : 0.003 0.039 2094 Dihedral : 5.288 32.041 1632 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.71 % Allowed : 13.25 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.21), residues: 1548 helix: 1.30 (0.19), residues: 738 sheet: 0.82 (0.48), residues: 150 loop : -0.54 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 120 HIS 0.003 0.001 HIS C 119 PHE 0.010 0.002 PHE C 279 TYR 0.013 0.002 TYR F 112 ARG 0.003 0.001 ARG F 272 Details of bonding type rmsd hydrogen bonds : bond 0.04480 ( 572) hydrogen bonds : angle 4.60522 ( 1578) covalent geometry : bond 0.00330 (11970) covalent geometry : angle 0.52335 (16098) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 1.434 Fit side-chains REVERT: A 77 GLU cc_start: 0.8178 (OUTLIER) cc_final: 0.7499 (mm-30) REVERT: A 101 LYS cc_start: 0.7816 (mmtt) cc_final: 0.7422 (ptpp) REVERT: A 220 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7792 (mp0) REVERT: B 216 GLU cc_start: 0.7965 (pm20) cc_final: 0.7748 (pm20) REVERT: C 77 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7568 (mm-30) REVERT: C 101 LYS cc_start: 0.7725 (pttm) cc_final: 0.7357 (ptpp) REVERT: D 77 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7574 (mm-30) REVERT: E 77 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7459 (mm-30) REVERT: E 215 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8431 (t) REVERT: E 216 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7268 (mp0) REVERT: E 220 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7778 (mp0) REVERT: F 77 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7567 (mm-30) REVERT: F 101 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7250 (mptt) outliers start: 21 outliers final: 8 residues processed: 203 average time/residue: 1.4464 time to fit residues: 314.2815 Evaluate side-chains 199 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 231 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 29 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 155 optimal weight: 0.0030 chunk 73 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 53 ASN B 125 GLN D 125 GLN F 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.122395 restraints weight = 10464.623| |-----------------------------------------------------------------------------| r_work (start): 0.3421 rms_B_bonded: 1.11 r_work: 0.3301 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11970 Z= 0.234 Angle : 0.622 7.768 16098 Z= 0.348 Chirality : 0.049 0.160 1836 Planarity : 0.004 0.042 2094 Dihedral : 5.616 32.174 1632 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.63 % Allowed : 13.74 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.21), residues: 1548 helix: 1.15 (0.19), residues: 738 sheet: 0.16 (0.48), residues: 162 loop : -0.49 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 120 HIS 0.002 0.001 HIS C 119 PHE 0.012 0.002 PHE D 33 TYR 0.015 0.002 TYR A 137 ARG 0.004 0.001 ARG F 197 Details of bonding type rmsd hydrogen bonds : bond 0.05413 ( 572) hydrogen bonds : angle 4.80588 ( 1578) covalent geometry : bond 0.00528 (11970) covalent geometry : angle 0.62167 (16098) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 1.284 Fit side-chains REVERT: A 77 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7518 (mm-30) REVERT: A 101 LYS cc_start: 0.7897 (mmtt) cc_final: 0.7504 (ptpp) REVERT: A 220 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7797 (mp0) REVERT: B 77 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7522 (mm-30) REVERT: B 216 GLU cc_start: 0.7966 (pm20) cc_final: 0.7743 (pm20) REVERT: C 77 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7544 (mm-30) REVERT: D 77 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7599 (mm-30) REVERT: E 77 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7466 (mm-30) REVERT: E 215 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8493 (t) REVERT: E 216 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7302 (mp0) REVERT: E 220 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7790 (mp0) REVERT: F 77 GLU cc_start: 0.8226 (OUTLIER) cc_final: 0.7579 (mm-30) REVERT: F 101 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7214 (mptt) outliers start: 20 outliers final: 9 residues processed: 196 average time/residue: 1.4785 time to fit residues: 309.7714 Evaluate side-chains 198 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 77 GLU Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 231 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 67 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 140 optimal weight: 10.0000 chunk 135 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 116 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN D 125 GLN D 205 GLN F 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.145675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.123088 restraints weight = 10456.678| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.11 r_work: 0.3304 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11970 Z= 0.198 Angle : 0.583 7.542 16098 Z= 0.326 Chirality : 0.047 0.135 1836 Planarity : 0.004 0.038 2094 Dihedral : 5.498 32.158 1632 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.54 % Allowed : 13.98 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.21), residues: 1548 helix: 1.20 (0.19), residues: 738 sheet: 0.18 (0.48), residues: 162 loop : -0.45 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP C 120 HIS 0.002 0.001 HIS D 119 PHE 0.010 0.002 PHE B 94 TYR 0.013 0.002 TYR A 137 ARG 0.003 0.001 ARG C 197 Details of bonding type rmsd hydrogen bonds : bond 0.05029 ( 572) hydrogen bonds : angle 4.71407 ( 1578) covalent geometry : bond 0.00443 (11970) covalent geometry : angle 0.58282 (16098) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3096 Ramachandran restraints generated. 1548 Oldfield, 0 Emsley, 1548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 1.296 Fit side-chains REVERT: A 77 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7515 (mm-30) REVERT: A 101 LYS cc_start: 0.7884 (mmtt) cc_final: 0.7481 (ptpp) REVERT: A 220 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7811 (mp0) REVERT: B 216 GLU cc_start: 0.8023 (pm20) cc_final: 0.7795 (pm20) REVERT: B 282 LYS cc_start: 0.7668 (OUTLIER) cc_final: 0.7317 (mptt) REVERT: C 77 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7572 (mm-30) REVERT: C 101 LYS cc_start: 0.7762 (pttm) cc_final: 0.7409 (ptpp) REVERT: D 77 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7595 (mm-30) REVERT: E 77 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7458 (mm-30) REVERT: E 215 VAL cc_start: 0.8753 (OUTLIER) cc_final: 0.8487 (t) REVERT: E 216 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7306 (mp0) REVERT: E 220 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7790 (mp0) REVERT: F 77 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7562 (mm-30) REVERT: F 101 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7249 (mptt) outliers start: 19 outliers final: 9 residues processed: 195 average time/residue: 1.4666 time to fit residues: 305.8366 Evaluate side-chains 196 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 210 SER Chi-restraints excluded: chain B residue 74 LYS Chi-restraints excluded: chain B residue 118 LYS Chi-restraints excluded: chain B residue 231 SER Chi-restraints excluded: chain B residue 282 LYS Chi-restraints excluded: chain C residue 77 GLU Chi-restraints excluded: chain C residue 231 SER Chi-restraints excluded: chain D residue 77 GLU Chi-restraints excluded: chain E residue 77 GLU Chi-restraints excluded: chain E residue 209 VAL Chi-restraints excluded: chain E residue 210 SER Chi-restraints excluded: chain E residue 215 VAL Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain F residue 77 GLU Chi-restraints excluded: chain F residue 101 LYS Chi-restraints excluded: chain F residue 231 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 128 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 118 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 125 GLN D 125 GLN D 205 GLN F 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.146684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.124097 restraints weight = 10403.186| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 1.11 r_work: 0.3327 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11970 Z= 0.156 Angle : 0.542 7.452 16098 Z= 0.301 Chirality : 0.045 0.139 1836 Planarity : 0.004 0.039 2094 Dihedral : 5.300 32.757 1632 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.71 % Allowed : 13.74 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1548 helix: 1.31 (0.19), residues: 738 sheet: 0.83 (0.48), residues: 150 loop : -0.50 (0.21), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 120 HIS 0.005 0.001 HIS A 119 PHE 0.009 0.002 PHE B 94 TYR 0.014 0.002 TYR F 112 ARG 0.003 0.001 ARG F 272 Details of bonding type rmsd hydrogen bonds : bond 0.04570 ( 572) hydrogen bonds : angle 4.58061 ( 1578) covalent geometry : bond 0.00344 (11970) covalent geometry : angle 0.54184 (16098) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9525.35 seconds wall clock time: 164 minutes 25.65 seconds (9865.65 seconds total)